Contacts of the helix formed by residues 218 - 230 (chain A) in PDB entry 5IVK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLU* 1.3 80.5 - - - +
219A ALA* 1.3 57.3 + - - -
221A ALA* 2.8 19.9 + - - +
222A ALA 2.9 10.9 + - - -
243A MET 2.9 13.1 + - - -
244A SER 3.1 15.0 + - - -
251A TRP* 3.4 11.2 - - - -
471A HIS* 3.0 20.3 + - - -
601A DPF 1.6 53.2 + - - -
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A HIS 4.4 0.9 - - - -
135A GLY* 3.9 7.2 - - - -
137A GLY* 3.6 16.6 - - - +
138A PHE* 3.6 33.3 - - + +
165A TYR* 4.8 2.0 - - - +
217A GLU 3.2 0.4 + - - -
218A SER* 1.3 78.8 + - - +
220A GLY* 1.3 56.9 + - - +
222A ALA* 3.8 0.4 - - - -
223A SER* 2.8 30.4 + - - -
251A TRP* 3.8 12.4 - - + -
601A DPF 3.0 16.7 + - - +
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Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 3.2 24.3 - - - +
134A HIS 3.6 7.4 - - - -
135A GLY* 3.4 3.8 - - - -
216A GLY* 3.5 8.9 - - - -
217A GLU 2.9 9.9 + - - -
219A ALA* 1.3 77.9 - - - +
221A ALA* 1.3 58.2 + - - +
223A SER* 3.5 6.8 - - - -
224A THR* 2.9 31.0 + - - -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLY 3.3 23.2 - - - +
217A GLU 3.5 0.2 - - - +
218A SER 2.8 10.3 + - - +
220A GLY* 1.3 76.1 - - - +
222A ALA* 1.3 64.7 + - - +
224A THR* 3.3 4.2 + - - -
225A HIS* 2.9 21.3 + - - +
242A LEU* 3.5 10.7 - - - +
243A MET 3.3 24.2 - - - +
245A GLY 3.4 22.8 - - - +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE* 4.1 9.2 - - + -
218A SER 2.9 6.5 + - - -
219A ALA 3.8 6.5 - - - +
221A ALA* 1.3 75.7 - - - +
223A SER* 1.3 57.7 + - - +
225A HIS* 3.2 3.1 + - - +
226A TYR* 2.8 38.1 + - + -
246A ASN 3.8 29.2 - - - +
247A ALA* 4.4 0.3 - - - +
251A TRP* 4.0 14.1 - - + -
252A ALA* 3.9 19.1 - - + -
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 3.6 12.4 - - - +
138A PHE* 3.3 13.2 - - - -
165A TYR* 4.5 1.2 + - - -
188A LEU* 4.2 1.0 - - - +
191A GLN* 3.0 36.6 + - - +
219A ALA 2.8 24.1 + - - -
220A GLY 3.5 5.8 - - - -
221A ALA 3.2 0.2 - - - -
222A ALA* 1.3 74.1 - - - +
224A THR* 1.3 66.9 + - - +
226A TYR* 3.1 10.8 + - - +
227A MET* 2.9 29.2 + - - +
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Residues in contact with THR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 4.1 3.0 - - - +
214A VAL* 3.4 45.3 - - + +
215A PHE 3.3 19.4 + - - -
220A GLY 2.9 19.0 + - - -
221A ALA* 3.7 5.6 - - - -
223A SER* 1.3 74.7 - - - +
225A HIS* 1.3 62.6 + - - +
227A MET* 3.2 4.9 + - - +
228A MET* 3.0 31.8 + - + +
240A GLY* 4.5 0.4 - - - -
241A ILE 4.0 6.5 - - - +
242A LEU* 3.5 18.4 - - + -
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Residues in contact with HIS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ALA 2.9 17.4 + - - +
222A ALA 3.5 4.9 - - - +
224A THR* 1.3 78.3 - - - +
226A TYR* 1.3 62.3 + - - +
228A MET* 2.9 24.4 + - + +
229A LEU* 3.0 47.1 + - + +
242A LEU* 3.7 24.1 - - + +
246A ASN* 3.6 5.7 - - + +
247A ALA* 2.9 30.3 + - + +
248A ILE* 4.6 3.6 - - + -
333A VAL* 4.4 4.3 - - + -
339A ASN* 5.3 2.8 + - - -
345A MET* 5.9 0.2 - - + -
428A LEU* 3.5 37.1 - - + +
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Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE* 4.4 0.7 - + - -
188A LEU* 3.9 29.6 - - + -
222A ALA* 2.8 37.9 + - + -
223A SER* 3.6 5.8 - - - +
225A HIS* 1.3 71.3 - - - +
227A MET* 1.3 63.8 + - + +
229A LEU* 3.0 22.1 + - + +
230A THR* 3.0 19.1 + - - +
247A ALA* 3.3 29.6 + - + +
252A ALA 2.6 27.6 + - - -
253A ASN* 3.2 16.3 - - - +
313A PRO* 3.7 22.4 - - + -
324A VAL* 4.9 1.0 - - + +
325A LEU* 3.4 34.0 - - + +
329A PRO* 4.0 9.9 - - + -
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Residues in contact with MET 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 4.3 9.0 - - + -
188A LEU* 3.7 35.7 - - + +
191A GLN* 3.8 26.0 - - - +
192A VAL* 3.7 25.1 - - + -
195A LEU* 3.7 32.8 - - + -
214A VAL* 5.1 1.1 - - + -
223A SER 2.9 16.5 + - - +
224A THR* 3.6 9.2 - - - +
225A HIS 3.2 0.2 - - - -
226A TYR* 1.3 80.7 - - + +
228A MET* 1.3 57.3 + - - +
229A LEU 3.3 0.2 - - - -
230A THR* 4.3 1.3 - - + -
233A THR* 2.5 30.2 + - - -
237A PHE* 3.7 9.0 - - + -
324A VAL* 4.5 5.4 - - + -
337A TRP* 3.5 7.6 - - - -
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Residues in contact with MET 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A THR* 3.0 31.9 + - - +
225A HIS* 2.9 21.1 + - + +
227A MET* 1.3 76.6 - - - +
229A LEU* 1.3 60.6 + - - +
237A PHE* 3.6 20.0 - - + -
240A GLY* 4.2 11.4 - - - -
242A LEU* 4.2 12.8 - - + -
336A ALA* 3.9 3.5 - - - +
337A TRP* 3.6 10.8 + - - -
338A GLY* 2.9 51.7 + - - +
341A ILE* 4.2 11.0 - - + -
343A THR* 3.6 32.8 - - + +
345A MET* 6.1 0.4 - - + -
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A HIS* 3.0 48.5 + - + +
226A TYR* 3.0 16.0 + - + +
228A MET* 1.3 81.1 - - + +
230A THR* 1.3 65.1 + - - +
231A GLU* 3.6 5.5 + - - +
247A ALA* 4.1 16.8 - - + -
329A PRO* 4.4 9.4 - - + +
332A MET* 3.8 33.0 - - + +
333A VAL* 3.8 19.7 - - + +
335A THR 5.4 0.2 - - - -
336A ALA* 3.6 34.9 - - + +
337A TRP* 4.5 1.8 - - - -
339A ASN* 4.7 3.4 - - - +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 4.7 3.4 - - + -
226A TYR 3.0 14.6 + - - +
227A MET* 4.2 2.5 - - + +
229A LEU* 1.3 78.1 - - - +
231A GLU* 1.3 66.0 + - - +
232A GLN* 3.2 24.4 + - + +
233A THR* 3.2 29.3 + - + +
323A CYS 4.2 0.5 + - - -
324A VAL* 3.0 39.0 + - + -
332A MET* 3.8 8.7 - - - -
337A TRP* 3.1 22.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il